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For some reason when I open an old file, TextMate does not open it on a new tab; it opened the file in a new window??
For some reason when I open an old file, TextMate does not open it on a new tab; it opened the file in a new window??
= text to speech =
[https://nosrac.github.io/Dictater/ Dictate]


= Developer =
= Developer =

Revision as of 20:47, 9 July 2017

macOS

https://en.wikipedia.org/wiki/MacOS

Darwin (operating system) and release history

Find OS version by command line

$ sw_vers
ProductName:	Mac OS X
ProductVersion:	10.11.6
BuildVersion:	15G1004

$ sw_vers -productVersion
10.11.6

How to differentiate Linux and Mac

Use uname (unix name) with -s (system name) flag 

# Mac
$ uname -s
Darwin

# Linux
$ uname -s
Linux

BSD and Linux

What’s the Difference Between Linux and BSD?

Darwin, MacOS, OpenSource?

http://superuser.com/questions/19492/is-mac-os-x-open-source. Darwin is like Linux, FreeBSD, etc... Mac OS X GUI is like KDE, GNome, etc...

Apple Open Source https://opensource.apple.com/. It includes Kernel, macOS, Developer Tools, etc.

Partition format

fdisk will show it is HFS/ HFS+ 

/dev/sdb1  *       64 250675199 250675136 119.5G af HFS / HFS+

However, I got a problem when I run cp command. 

$ ls -l /media/brb/SamsungUSB/
-rw------- 1 99 99 10592270336 Feb 26 09:45 macSierra.ova
-rw-r--r-- 1 99 99  6922018816 Feb 15 14:40 Sierra10.12.3.iso
$ md5sum '/media/brb/SamsungUSB/macSierra.ova' 
md5sum: /media/brb/SamsungUSB/macSierra.ova: Permission denied

$ sudo chown brb /media/brb/SamsungUSB/macSierra.ova 
chown: changing ownership of '/media/brb/SamsungUSB/macSierra.ova': Read-only file system

Some suggestion is to disable journaled file system as this.

But I found the problem should be resolved in macOS. That is, running 'sudo chmod 644' on the file from an Mac computer.

Beta version of macOS

How to get the new version of macOS 10.13

Preferences - Energy Saver

OS X File System

Home directory

/Users/USERNAME

The following is the default directories under $HOME. 

$ ls ~/
Applications	Documents	Library		Music		Public	
Desktop		Downloads	Movies		Pictures

See also How to reclaim the /home directory.

/ (root) directory

Some directory may be hidden. See http://www.westwind.com/reference/OS-X/invisibles.html 

$ ls -l /
total 45
drwxrwxr-x+ 62 root  admin  2108 Feb 15 12:41 Applications
drwxr-xr-x+ 69 root  wheel  2346 Feb  9 11:02 Library
drwxr-xr-x@  3 root  wheel   102 Feb  9 08:47 Network
drwxr-xr-x@  4 root  wheel   136 Sep 16 17:07 System
drwxr-xr-x   7 root  admin   238 Feb  7 15:32 Users
drwxrwxrwt@  4 root  admin   136 Feb 15 13:32 Volumes
drwxr-xr-x@ 39 root  wheel  1326 Jul  8  2016 bin
drwxrwxr-t@  2 root  admin    68 Sep 16 16:59 cores
dr-xr-xr-x   3 root  wheel  4311 Feb  9 08:47 dev
lrwxr-xr-x@  1 root  wheel    11 Sep 16 16:59 etc -> private/etc
dr-xr-xr-x   2 root  wheel     1 Feb 14 15:31 home
-rw-r--r--@  1 root  wheel   313 Aug  2  2015 installer.failurerequests
dr-xr-xr-x   2 root  wheel     1 Feb 14 15:31 net
drwxr-xr-x@  3 root  wheel   102 Feb  9 14:58 opt
drwxr-xr-x@  6 root  wheel   204 Sep 16 16:59 private
drwxr-xr-x@ 59 root  wheel  2006 Sep 16 16:59 sbin
lrwxr-xr-x@  1 root  wheel    11 Sep 16 16:59 tmp -> private/tmp
drwxr-xr-x@ 12 root  wheel   408 Feb  9 11:02 usr
lrwxr-xr-x@  1 root  wheel    11 Sep 16 16:59 var -> private/var

Library folder & show hidden files/folders

How to show hidden files and folders including ~/Library on a Mac

In MacOS Sierra, use CMD-Shift-. (dot).

Or follow Quickly Show/Hide Hidden Files on macOS Sierra, OS X El Capitan & Yosemite

/Volumes and Machintosh HD directory

Macintosh HD is just a symbolic link to / (root) on your system; that is done in /Volumes. 

$ ls -l /Volumes/
total 8
lrwxr-xr-x  1 root  admin    1 Feb  9 08:47 Macintosh HD -> /
drwxrwxr-t  8 root  admin  340 Jan 18 14:06 OS X Install ESD

/Users/Shared folder

macOS Sierra: Share files with others who use your Mac

ExFat: Best drive/partition format to share data between Mac, Linux and OS X

http://superuser.com/questions/398190/what-is-the-best-drive-format-to-share-data-between-mac-linux-and-os-x

  • Mac OS doesn't support writing to NTFS drives.
  • NTFS and REFS are a bad choice because Linux and Mac can't properly decode it
  • exFAT doesn't support symlinks
  • Fat32 has a 4GB single file limit and 2TB partition size.
  • In one case when my NTFS partition (USB drive) is broken, it becomes a format called 'RAW' shown on Windows Disk Management utility.
  • It is easy to create exfat partition format on Windows 7. When I move the USB drive to a Linux machine, fdisk -l shows
$ sudo fdisk -l /dev/sdc
WARNING: GPT (GUID Partition Table) detected on '/dev/sdc'! The util fdisk doesn't support GPT. Use GNU Parted.

Disk /dev/sdc: 123.6 GB, 123633401856 bytes
255 heads, 63 sectors/track, 15030 cylinders, total 241471488 sectors
Units = sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 512 bytes / 512 bytes
Disk identifier: 0x5b508967

   Device Boot      Start         End      Blocks   Id  System
/dev/sdc1            2048   241469439   120733696    7  HPFS/NTFS/exFAT

For some reason using Disk Utility to erase/format a 16GB USB drive to ExFat failed (Media kit reports not enough space on device). Fortunately the command line method works (and fast at least for the 16GB space case). 

diskutil list     # get the name to the disk you're trying to format
diskutil unmountDisk force disk2
sudo dd if=/dev/zero of=/dev/disk2 bs=1024 count=1024
diskutil partitionDisk disk2 GPT ExFat "toshiba" 0g

rsync: mkstemp FILENAME failed: Function not implemented (38)

http://blog.marcelotmelo.com/linux/ubuntu/rsync-to-an-exfat-partition/ 

# Do not use 'rsync -av SRC DEST'

# Use
rsync -rltDv  --info=progress2 SRC DEST

What is the “wheel” user in OS X?

wheel is the system administrator group in BSD, much like root is the system administrator user. See http://superuser.com/questions/191955/what-is-the-wheel-user-in-os-x

/bin/sh and /bin/bash differences

https://discussions.apple.com/thread/3177477?start=0&tstart=0

How to Auto-Hide the Dock With No Delay

http://www.makeuseof.com/tag/auto-hide-dock-no-delay-mac/

How can I list my open network ports with netstat?

http://apple.stackexchange.com/questions/117644/how-can-i-list-my-open-network-ports-with-netstat 

sudo lsof -i -P | grep -i "listen"

Root account vs admin account

@ sign in file attributes

# seqtools-dl is a folder extracted from the SeqTools zip file.

# Case 1. the zip file is downloaded through a browser
brbs-iMac:~ brb$ ls -l@ Documents/seqtools-dl/SeqTools.app/Contents/MacOS/code
total 176
-rwxr-xr-x  1 brb  staff  18229 May 15 09:15 createGeneListSNPEFF.sh
-rwxr-xr-x  1 brb  staff   1550 Oct 24  2016 gdown.pl
-rwxr-xr-x  1 brb  staff   4214 May 15 09:15 gdown_mac.sh
-rwxr-xr-x  1 brb  staff  22264 May 15 09:15 statsVariantGeneAnno_Auto.sh
...

# Case 2. the zip file is obtained through the scp command
brbs-iMac:~ brb$ ls -l@ Downloads/seqtools-dl/SeqTools.app/Contents/MacOS/code
total 176
-rwxr-xr-x@ 1 brb  staff  18229 May 15 09:15 createGeneListSNPEFF.sh
	com.apple.quarantine	   57
-rwxr-xr-x@ 1 brb  staff   1550 Oct 24  2016 gdown.pl
	com.apple.quarantine	   57
-rwxr-xr-x@ 1 brb  staff   4214 May 15 09:15 gdown_mac.sh
	com.apple.quarantine	   57
-rwxr-xr-x@ 1 brb  staff  22264 May 15 09:15 statsVariantGeneAnno_Auto.sh
	com.apple.quarantine	   57
...

Create a Bootable macOS Installer

Make sure you use a USB flash drive or other removable media that has at least 12GB of available disk space. 

sudo /Applications/Install\ macOS\ Sierra.app/Contents/Resources/createinstallmedia \
     --volume /Volumes/usb16g --applicationpath /Applications/Install\ macOS\ Sierra.app

Reboot, holding down the OPTION key and selecting the “Install OS X Sierra” drive upon boot..

Install to a USB drive

To boot from your external Sierra drive, plug it into the Mac in question, press the power button, and hold the Option key until the recovery disk screen appears. From there, you can select your external drive and click the arrow to boot into it for that session.

How to Install and Use macOS Sierra on an External Drive

https://www.howtogeek.com/293476/how-to-install-and-use-macos-sierra-on-an-external-drive/

How to Burn OS X El Capitan to a USB Flash Drive

http://lifehacker.com/how-to-burn-os-x-el-capitan-to-a-usb-flash-drive-1733425133

Install, Boot, and Run Mac OS X From an External Hard Drive

http://www.online-tech-tips.com/mac-os-x/install-boot-and-run-mac-os-x-from-an-external-hard-drive/

Terminal

Where is the terminal

Macintosh HD/Applications/Utilities/Terminal.

Keyboard symbols

Keyboard shortcuts

  • Ctrl + a - going to the beginning of the line
  • Ctrl + e - going to the end of the line
  • Fn + Down arrow = page down
  • Fn + Up arrow = page up

Rename terminal tabs

Click the “Shell” menu and select “Edit Title” to bring up the Terminal Inspector window

Terminal replacement

  • iTerm2. Good. The HOME/END keys work when I work in a virtual machine. To change font size, go to Preferences -> Profile -> Text -> Font or just use the keyboard shortcut Command + +/-.
  • MacTerm

exit does not close a terminal/tab

You can change the setting by Preferences -> Profiles -> Shell. See https://superuser.com/questions/158375/how-do-i-close-the-terminal-in-osx-from-the-command-line.

Mac Terminal’s Hidden Task Manager to See Background Processes

https://www.howtogeek.com/309273/how-to-use-the-mac-terminals-hidden-task-manager-to-see-background-processes/

terminal fun

Keyboard shortcuts

How Not Using Keyboard Shortcuts Makes You Lose 64 Hours Every Year

Keyboard mappings using a PC keyboard on a Macintosh

Mac keyboard: Ctrl -> Option/Alt -> Cmd. Windows keyboard: Ctrl -> Windows -> Alt.

Mac-keyboard.jpg Windows-keyboard.jpg

Lock screen

Shift + control + power

Minimize all windows

  • Method 1: Cmd + F3 (min apps go to the RHS)
  • Method 2: Opt + Cmd + H + M

Finder

Command + [: move back to the previous folder

See more.

Navigation in a browser or document

  • Command + up = go to the top of the document
  • Command + down = go to the end of the document
  • Command + f = search
  • Fn + Down arrow = page down (or Spacebar in a web browser)
  • Fn + Up arrow = page up (or Shift + Spacebar in a web browser)
  • Fn + Left arrow = Home
  • Fn + Right arrow = End

Text navigation and selection

12 Keyboard Shortcuts for Navigating & Selecting Text in Mac OS X

  • Select text to beginning of a line – Shift+Command+Left Arrow
  • Select text to end of a line – Shift+Command+Right Arrow
  • Select text to beginning of current word – Shift+Option+Right Arrow
  • Select text to end of current word – Shift+Option+Right Arrow
  • Select text to beginning of all text – Shift+Command+Up Arrow
  • Select text to end of all text – Shift+Command+Down Arrow

Switch input sources

Go to System Preferences -> Keyboard -> Shortcuts -> Input Sources. Check 'Select the previous input source ^Space'. Use Ctrl + Space to switch.

Compare to Windows/Linux

  • Use Command + q to close an application instead of "Alt+F4" on Windows/Linux.
  • System Activity tool:
    • Windows: Task Manager
    • Linux: System Monitor
    • Mac: Activity Monitor

Hardware

2015 Macbook Pro model A1398, 15.4 inch.

Display resolution

2880x1800 on my 15-Inch Retina Display MacBook Pro. According to the Retina Display page on Wikipedia, its PPI (pixels per inch) is 220. To achieve the same PPI on 21.5 inch display, it has to be 4K and the display has to be 5K if it is 27 inch display.

Unfortunately Virtualbox (5.1.14) can only give 1440x900 (tested on Ubuntu & Windows). See a workout http://tusharm.com/articles/win7-on-retina-display-with-virtual-box/.

Touchpad

Need to press a little bit (instead of touch) for the left-click effect. If we want to use 'tap' for the click (like other OS), go to the System Preferences to change it.

The right click is called secondary click in OS X. By default it is click with two fingers. We can change the setting by going to System Preferences/Touchpad/Secondary click.

  • Scroll: two fingers move up/down. The direction is like moving a paper; i.e. scrolling up will gradually show the next part of the content.
  • Zoom in/out: pinch with two fingers.
  • Smart zoom: double-tap with two fingers.
  • Drag and drop method 1: Use the normal three finger drag, leave two fingers on the trackpad while doing a flicking motion with the third finger (eg thumb). The more momentum you add to your motion, the further it drags.
  • Drag and drop method 2:
    1. highlight the app first
    2. lightly click the app (you should only feel one click. Do not use too much force; if you do, you will hear two click sound and it will pop up a window to show the file information) with your thumb and then use your index to move the app to “Applications” directory.

CPU information

sysctl -n machdep.cpu.brand_string

My macbook Pro 2015 shows i7-4980HQ (see GeekBench 4 score) CPU @ 2.80GHz. Quad cores. Eight threads. Base Frequency 2.8GHz. Max Turbo Frequency 4.0GHz. Bus Speed: 5 GT/s DMI2.

Power Adapter

85W MagSafe 2 Power Adapter for MacBook Pro with Retina Display (MD506LL/A) $75

iMac Pro

The new (2017) iMac Pro can be equipped with a 128 GB of memory and 4 TB SSD drive.

Finder - file manager

Enter key does not open the file

Use Command+Down instead of Enter key to open a file or go into a directory.

Enter key is only used to rename a file. See https://discussions.apple.com/thread/3140356?start=0&tstart=0.

Use Command+Down will immediately uncompress a tar.gz file.

Go to a folder

Use Cmd+Shift+o to go to a specific location by entering its full path. Unfortunately this option is not available in other applications in general.

Commander One

Free dual pane file manager for Mac.

  • User Guide
  • The bookmark is called 'Favorites' in Commander One. Click the 'star' icon and a Windows' style of a right click menu will pop up. You can select 'Add to Favorites' to add the current directory to the favorites. This bookmarked location will be shown when you click the 'star' icon next time.
  • The icon (multiple horizontal lines) next to the 'star' shows the recent locations. This is useful too!
  • By default, Commander One will send anonymous usage statistics to Eltima. Go to Preferences -> General to uncheck this option.

Screenshots

http://www.howtogeek.com/278615/the-best-screenshot-apps-for-macos/

Terminal

Use the screencapture command. 

screencapture test.jpg

screencapture -c    # send to the clipboard

screencapture -T 10 timedshot.jpg # timer 

screencapture -w test.jpg
# OR
screencapture -W

screencapture -h     # help

To view an image file, use the open command. See also Shell tricks: the OS X open command. 

open test.jpg

Grab

Take a Timed Screenshot With the Grab (built-in) Application. Open Grab, select Capture -> Selection/Window/Screen/Timed screen.

Lightshot

Lightshot works like Shutter in Ubuntu - easy to use and can sit on the taskbar.

Note: to view an image resolution in Finder, right click an image and select Get Info -> More Info.

Screen cast

Quicktime player

We can record the screen (full screen or a selected region). The recorded file will be in a .mov format.

Screen cast o magic

http://screencast-o-matic.com/

Application

How to Install Applications

Keyboard shortcut to launch an application

  • F4 key - LaunchPad
  • Command + Space - Spotlight search

Messages when you launch an application

  • Google Chrome

ChromeMac.png

  • iTerm

Iterm open.png

  • SeqTools

Seqtoos open1.png Seqtoos open2.png Seqtoos open3.png

Install pkg file from command line

http://apple.stackexchange.com/questions/15658/how-can-i-open-a-pkg-file-manually 

sudo installer -pkg ~/Downloads/packagename.pkg -target ~/Applications/
# OR
installer -pkg ~/Downloads/packagename.pkg -target ~/Applications/

Close an application

Clicking the red button does close/quit an application/a program. You need to use Command-Q.

Another answer: The red close button just closes the window. It is up to the application whether it quits or not - typically if the application uses documents or it has other windows that can be opened it will not quit. Applications with a single window (System Preferences, for example), will usually quit when the window is closed, since there isn't anything else it does.

Package formats

app directory

Example: App Store.app, Atom editor, SourceTree

http://apple.stackexchange.com/questions/112197/what-does-a-app-file-actually-do

apps are "Package Bundles" is Apple jargon. These are actually Unix directories, in a special format. The actual Unix Executable File is in a subdirectory named MacOS, which you can see using the "Show Package Contents" menu in Finder.

To deliver the program in an app format, we can zip the app folder. If we use Safari browser, it will automatically decompress the zip file so the app program will appear in the Downloads directory.

For example, in SourceTree, the download file is called 'SourceTree_X.Y.zip'. When we click the zip file, it will be automatically extracted. And when I click SourceTree.app, it will have a dialog to help user to move the program to the application folder.

Sourcetree.png

pkg file

Example: R-cran

PKG files are Mac OS X installation (setup) packages that contain installer scripts ('Scripts' file) and compressed installation files ('Payload' file) that are used to install Mac software applications onto a user's hard drive.

On the case of R-x.y.z.pkg, it contains R framework, R.app GUI, Tcl/Tk X11 and TexInfo.

To install a pkg file from terminal, see this post 

sudo installer -pkg R-3.3.3.pkg -target /

dmg (disk image) file

Example: Google chrome, JDK, FastQC, Sketchup, Commander One.

A DMG file is a disk image, which is sort of like an archive file. When you download one, you can double-click it to “mount” it (under Devices in the Finder), allowing you to extract the application from inside it.

After the app is dragged to your Applications folder, you can run it normally — from the Finder, Launchpad, Spotlight, dock, or anything else.

We can mount or eject a dmg file by 

# mount
hdiutil mount fastqc_v0.11.5.dmg
# copy its content
mkdir -p ~/FastQC
cp -r /Volumes/FastQC/FastQC.app/Contents/MacOS/* ~/FastQC/
# eject
hdiutil eject /Volumes/FastQC/

To create a dmg file (see command line or here and GUI) 

hdiutil create -volname WhatYouWantTheDiskToBeNamed \
    -srcfolder /path/to/the/folder/you/want/to/create \
    -ov -format UDZO name.dmg

To convert a dmg file to iso 

hdiutil convert imagefile.dmg -format UDTO -o imagefile.iso
mv imagefile.iso.cdr imagefile.iso

To install a dmg file from terminal, see this or this 

MOUNTDIR=$(echo `hdiutil mount jdk-8u121-macosx-x64.dmg | tail -1 \
| awk '{$1=$2=""; print $0}'` | xargs -0 echo) \
&& sudo installer -pkg "${MOUNTDIR}/"*.pkg -target / \
&& sudo hdiutil detach "${MOUNTDIR}"

Explanation: The first command (hdiutil mount jdk-8u121-macosx-x64.dmg) will output 

expected   CRC32 $628D96B6
/dev/disk2          	GUID_partition_scheme          	
/dev/disk2s1        	Apple_HFS                      	/Volumes/JDK 8 Update 121

We like to grab the string "/Volumes/JDK 8 Update 121". This can be achieved by getting the last line of the output and replace the first and 2nd fields with empties and then output the whole line.

Package manage software

http://apple.stackexchange.com/questions/32724/what-are-pros-and-cons-for-macports-fink-and-homebrew & http://apple.stackexchange.com/questions/64690/macports-vs-fink-vs-homebrew

MacPorts

Different versions of Mac OS X has a different macport binary (in .pkg format).

Homebrew

# Install
/usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
# install some package
brew install wget
# Uninstall homebrew
ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/uninstall)"

Fink

No binary installer for recent versions of OS X (good to me). You will need to install the proper Command Line Tools for Xcode for your system.

Rudix

# install
curl -s https://raw.githubusercontent.com/rudix-mac/rpm/2016.12.13/rudix.py | sudo python - install rudix
# install some package
sudo rudix install wget
sudo rudix install python-pip
# remove a package
sudo rudix remove python-pip
# uninstall
sudo rudix -R

Text editor

http://beebom.com/best-text-editors-for-mac/

Change the default text editor

Just right (or control) click a file of the type you want to change and: "Get Info" -> "Open with:" -> (Select your program) -> "Change All"

If you use the open command in a terminal to open a text file, the default program will be used.

Atom editor from Github

Atom Flight Manual

  • The atom application requires no installation. So once it is downloaded (we actually download a zip file. After download has finished Safari browser will automatically decompress the zip file), we can drag it to the Application folder.
  • Open atom from a terminal.

Method 1 (GUI). Atom -> Install Shell Commands. Two symbolic links (atom and apm) will be created in /usr/local/bin to point to the currently opened Atom application.

Method 2 (Manual): 

ln -s /Applications/Atom.app/Contents/Resources/app/atom.sh /usr/local/bin/atom
  • When you open the Atom the first time, it will split the screen into two panes: on the LHS it has a 'Welcome' and on the RHS it has a 'Welcome Guide'. You can choose to close any one of them by View -> Panes -> Close Pane. You may reopen the Welcome Guide by Help -> Welcome Guide.
  • You can hide the directory on the left hand side by View -> Toggle Tree View.
  • Command Palette: Press Cmd+Shift+P.
  • Settings: Atom -> Preferences.
  • Open a file: Cmd+o. Save a file: Cmd+s.
  • If a file is modified and not saved yet, the changes are saved to a cache. Even we close Atom, the changes are there. The original file is still intact.
  • Open a directory as a project. Open a folder will add a tree view to the editor where you can browse all the files. You can toggle the tree view on the side of the window by Cmd+\.
  • Jump to a specific line: Ctrl+g.
  • Find and replace: Cmd+f. To search the whole project, Cmd+Shift+f.
  • Folding: Alt+Cmd+[ and Alt+Cmd+]
  • Panes splitting: Cmd+K Up/Down/Left/Right
  • Preview a markdown file (toggle): Ctrl+Shift+M
  • R syntax highlight
$ apm install language-r
Installing language-r to /Users/USERNAME/.atom/packages ✓
# Re-start Atom to enable it

Printing. No way!

Sublime

http://www.sublimetext.com/

TextMate

http://lifehacker.com/5817833/the-best-programming-text-editor-for-mac

For some reason when I open an old file, TextMate does not open it on a new tab; it opened the file in a new window??

text to speech

Dictate

Developer

Macs (unlike Linux) don’t come with a package manager, but there are a couple of popular package managers you can install. See SciPy.

Install Xcode

http://osxdaily.com/2014/02/12/install-command-line-tools-mac-os-x/

Note: it seems there is no way to run this automatically without the alert box. Users need to agree the license. 

xcode-select --install

The installed tools (like ar, gcc, g++, git, libtool, make, nm, otool, svn, et al) are located in /Library/Developer/CommandLineTools/usr/bin/ directory. If the command is run again, you will get a message 

xcode-select: error: command line tools are already installed, use "Software update" to install updates

To check the Xcode version (if you have installed a full Xcode) 

$ xcodebuild -version  # if you have the full Xcode installed
Xcode 8.2.1
Build version 8C1002  # if you only have the command line tool installed
$ xcodebuild -version
xcode-select: error: tool 'xcodebuild' requires Xcode, but active developer 
directory '/Library/Developer/CommandLineTools' is a command line tool instance

To check whether Xcode has been installed 

$ xcode-select -p
/Library/Developer/CommandLineTools             # if you have installed the command line tool only
# or
/Applications/Xcode.app/Contents/Developer  # if you have the full Xcode package installed
# or
xcode-select: error: unable to get active developer directory, use `sudo xcode-select --switch path/to/Xcode.app` to set one
(or see `man xcode-select`)

To accept the XCode license through command line, follow the post Debugging macOS Kernel using VirtualBox: 

$ sudo xcodebuild -license accept # it seems not working. A dialog is still popped up.

The df command shows installing the command line developer tools takes about 600MB space.

Uninstall Xcode

http://osxdaily.com/2012/02/20/uninstall-xcode/

Header file location

  • /usr/include
  • /usr/local/include (e.g. from "sudo make install" command)
  • /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.12.sdk/usr/include/ (if you have installed a full Xcode)

Lib location

  • /usr/lib
  • /usr/local/lib
  • /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.12.sdk/usr/lib/ (if you have installed a full Xcode)

ldd on Mac

otool -L  <exec>

openssl

Method 1: brew 

brew doctor
brew update
brew upgrade
brew install openssl  # the opposite operation is 'uninstall'
cd /usr/local/include
ln -s ../opt/openssl/include/openssl .

Method 2: compile yourself

Python packages

http://www.scipy.org/install.html

VirtualBox

Touchpad

The direction of scrolling up and down in guest machine is opposite to the host machine.

Keyboard shortcuts

Since there is no Command key on Windows keyboards, we need to modify preferences.

Copy and paste: go to preferences -> keyboard -> Modifier keys. Change 'Option' key to 'Command' key and 'Command' key to 'Option' key. Since the 'Option' key is 'Alt' on Windows keyboards, the layout will be very similar to using Mac keyboards. This is consistent with Logitech K780 multi-device keyboard where 'Alt' key shares with the 'Command' key.

Do not use Ctrl to replace Command; you will not able to use the Ctrl key in nano and you are missing Ctrl + a to move mouse to HOME in Terminals. NOTE: iTerm2 is a good replacement for macOS's built-in Terminal program; HOME/END works.

Guest additions

VirtualBox doesn't have guest additions for OSX. http://askubuntu.com/questions/372982/virtualbox-4-3-guest-additions-on-osx-guest

In order to share files between the host and guest machine, we need to 1. add 'host-only' network adapter to the guest machine and 2. enable 'Remote Login' by going to the System Preferences -> Sharing.

For example, from the host machine, I can use the following on the host machine to access the guest machine 

$ ssh [email protected]

However, it is unsuccessfully to do access the host machine from the guest machine?? 

$ ssh [email protected]

Smart card reader

If USB is enabled in the guest machine, the Smart Card reader will not be available on the host machine. That is, we cannot use the smart card in Mac. So it is necessary to uncheck the USB from the USB setting in the guest machine.

Windows Virtual Machine

  • Left CMD is used by VirtualBox to switch to full screen for example
  • Right CMD works like the Windows key

Screen resolution

https://forums.virtualbox.org/viewtopic.php?f=22&t=54030 works. 

$ VBoxManage setextradata "vm_name" VBoxInternal2/EfiGopMode 4

The number '3' corresponds to a resolution of 1280x1024 (5:4) and '4' corresponds to 1440x900 (8:5). On lenovo laptop (1600 x 900, 16:9), the height will fill the screen but there are little black spaces on both sides. See Display resolution and aspect ratio.

Note that I need to enable Full Screen for the guest machine b/c the desktop is too large.

El Capitan (10.11)

It works on my VirtualBox 5.1.14 and Macbook Pro 2015.

Note: if I skip the following commands, the macOS booting will keep re-run again and again. 

VBoxManage modifyvm macElcapitan --cpuidset 00000001 000106e5 00100800 0098e3fd bfebfbff
VBoxManage setextradata macElcapitan "VBoxInternal/Devices/efi/0/Config/DmiSystemProduct" "iMac11,3"
VBoxManage setextradata macElcapitan "VBoxInternal/Devices/efi/0/Config/DmiSystemVersion" "1.0"
VBoxManage setextradata macElcapitan "VBoxInternal/Devices/efi/0/Config/DmiBoardProduct" "Iloveapple"
VBoxManage setextradata macElcapitan "VBoxInternal/Devices/smc/0/Config/DeviceKey" "ourhardworkbythesewordsguardedpleasedontsteal(c)AppleComputerInc"
VBoxManage setextradata macElcapitan "VBoxInternal/Devices/smc/0/Config/GetKeyFromRealSMC" 1

Con: The image downloaded there is already a virtual machine image format.

If I try to use the iso file downloaded from internet, I saw an error "Missing Bluetooth Controller Transport" (https://gist.github.com/frdmn/de12c894a385bc8e6bff).

Sierra (10.12)

  1. The official image (e.g. Install macOS Sierra.app) we downloaded from Apple Store is saved under /Applications folder.
  2. We can follow the instruction https://github.com/geerlingguy/macos-virtualbox-vm to convert the app folder into an iso file. The prepare-iso.sh script seems to always put the iso file onto the Desktop folder; i.e. output folder and name is not taken.
  3. When we want to create a virtual machine in VirtualBox
    • video memory change from 16GB to 128MB
    • increase memory to 4096MB
    • turn off audio
VBoxManage modifyvm "{vmname}" --cpuidset 00000001 000306a9 00020800 80000201 178bfbff

Another instruction is to run (this seems to be necessary even we uses 'import Appliance' method) 

VBoxManage modifyvm "Sierra10.14" --cpuidset 00000001 000106e5 00100800 0098e3fd bfebfbff
VBoxManage setextradata "Sierra10.14" "VBoxInternal/Devices/efi/0/Config/DmiSystemProduct" "iMac11,3"
VBoxManage setextradata "Sierra10.14" "VBoxInternal/Devices/efi/0/Config/DmiSystemVersion" "1.0"
VBoxManage setextradata "Sierra10.14" "VBoxInternal/Devices/efi/0/Config/DmiBoardProduct" "Iloveapple"
VBoxManage setextradata "Sierra10.14" "VBoxInternal/Devices/smc/0/Config/DeviceKey" "ourhardworkbythesewordsguardedpleasedontsteal(c)AppleComputerInc"
VBoxManage setextradata "Sierra10.14" "VBoxInternal/Devices/smc/0/Config/GetKeyFromRealSMC" 1

After booting, select the preferred language and (before click the 'Continue' button) go to Utilities > Disk Utility. Select the VirtualBox disk and choose Erase to format it as a Mac OS Extended (Journaled) drive. Installing macOS took about 15 minutes on my Dell T3600 Desktop running Ubuntu/Mint.

After a successful login, the 'df -h' command shows macOS uses 8.6 GB space.

Unfortunately, the Mac guest machine cannot install guest additions.

I get a 'Guru meditation' error when I test the iso on an old non-mac machine (intel core 2 duo CPU).

Note there is an error (IOConsoleUsers: gIOScreenLockState 3, hs 0, bs 0, now 0, sm 0x0) to install Sierra 10.12.4 as a guest machine. See https://benlimmer.com/2017/04/23/macos-sierra-virtualbox-10-12-4/.

Create an ISO from the Sierra install app obtained from the Mac app store

https://klue.github.io/blog/2017/04/macos_kernel_debugging_vbox/

Remote connection (ssh)

Use Preferences -> Sharing -> Select Remote Login. http://osxdaily.com/2011/09/30/remote-login-ssh-server-mac-os-x/

To uses a command line to enable it, see

ssh key

Remote/Virtual machine: go to system preferences -> sharing and enable remote login. Suppose the user name is 'brb' and the hostname is 'brbs-MacBook-Pro.local'.

Host machine: 

ssh-keygen -t rsa -f ~/.ssh/virtmac  # press 'Enter' 3 times
cat ~/.ssh/virtmac.pub | ssh [email protected] "mkdir -p ~/.ssh && cat >>  ~/.ssh/authorized_keys"
ssh -i ~/.ssh/virtmac [email protected]

When I run testings, I need to restore the virtual machine to its initial status. I can use this method in order to avoid the message "WARNING: REMOTE HOST IDENTIFICATION HAS CHANGED!" when I use the 'ssh' command.

Remote Desktop Connection to Mac

On Mac, go to system preferences -> System Preferences -> Sharing -> Screen Sharing. It will show the vnc address of the Mac computer.

On my Ubuntu, see AppleRemoteDesktop

  • The built-in program Remmina Remote Desktop Client does not work. After clicking the 'connect' button & entering username/password, the screen flashed and disappeared.
  • RealVNC. I download the tarball (VNC Connect 6.0.3, Generic x64, default). Extract it to the Download folder and run vncviewer program. Yes, I can connect to Mac. But since the Mac has a very high resolution, I need to adjust the resolution setting in my connection. To do that: close the connection, right click a connection icon (created from last connection), choose Properties. In 'Options' tab, select Scaling -> Scale to fit window.
    • After connection, a toolbar will appear on the top of screen. It has a series of icons: Full screen mode, No scaling, Ctrl Alt Del, Info, Properties, Disconnect.
    • Even Mac screen lid is closed, VNC still works.
    • The connection speed is not ideal. You can see the screen refresh slowly.
  • Vinagre. It has to be installed from Ubuntu Software. Unfortunately it does not even allow me to enter a long password:(

Remote Desktop Connection from Mac

When I try to use the Screen Sharing (1.7) program in Mac to connect to Ubuntu 16.04 (type 'vnc://192.168.1.188'), I get an error 'The software on the remote computer appears to be incompatible with this version of Screen Sharing.'

Failscreensharing.png

Another remote desktop program is called Remote Desktop Connection for iMac. It appears to be used to connect to a Windows-based computer.

Tips

Got a New Mac? Do This First!

http://www.makeuseof.com/tag/new-mac-setup/

app Store

  • Need a credit card information. The 'None' option is not available. Some tricks.
  • Cannot log in my account. Activity clock just keeps spinning and spinning
  • If macOS has been downloaded, the 'Download' button will be changed to 'Open' button in 'App Store' application.
  • If my macOS is already Sierra, we don't need to sign into 'App Store' in order to download a newer version Sierra image.

Upgrading to macOS Sierra (nee OSX) for R users

http://www.win-vector.com/blog/2017/01/upgrading-to-macos-sierra-nee-osx-for-r-users/

Access the Root Directory

http://osxdaily.com/2013/01/17/access-root-directory-mac-os-x/

Disable update notification

http://news.softpedia.com/news/how-to-disable-os-x-update-notifications-493961.shtml

How to Configure a Proxy Server

https://www.howtogeek.com/293444/how-to-configure-a-proxy-server-on-a-mac/

Open a chm file

iChm program works fine. Chmox is too old (power pc) and not works.

CHM Reader from Mac App Store is not different from iChm.

Back up

Record sound

Use 'QuickTime player'.

The build-in microphone is located inside the left speaker. The recording sound is weak. Go to System Preferences -> Sound. Select 'Input' tab and increase the 'input volume' from the smallest to the loudest.

If we want to use an external mic, make sure the headphone connector has 4 sections.

XXX can't be opened because it is from an unidentified developer

/private/var/folders

https://discussions.apple.com/thread/1933443?start=0&tstart=0

If SeqTools was downloaded through a browser, then when we launch it the R script folder in <run_variantannose.sh> becomes something like /private/var/folders/1h/kcm8vkdx6nl00z5wjm5bqlw00000gp/T/AppTranslocation/051E078E-7C2D-4C6C-90FF-F651985EC9C0/d/SeqTools.app/Contents/MacOS/SeqTools/code

Git GUI Client

https://git-scm.com/download/gui/mac

SourceTree

sourcetree. See also Happy Git and Gihub for the useR from Jenny Bryan.

Unfortunately it requires a Bitbucket account in order to finish its installation.

Github Desktop

Looks good. It is OK to bypass to login a Github account in the installation process.

Missing Linux commands

wget

Method 1: Rudix 

curl -O https://raw.githubusercontent.com/rudix-mac/rpm/2016.12.13/rudix.py
python rudix.py install rudix
sudo rudix install wget
which wget
# /usr/local/bin/wget

$ wget https://raw.githubusercontent.com/arraytools/bdge/master/install_rnaseq.sh
--2017-02-26 08:41:09--  https://raw.githubusercontent.com/arraytools/bdge/master/install_rnaseq.sh
Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 151.101.192.133, 151.101.128.133, 151.101.0.133, ...
Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|151.101.192.133|:443... connected.
ERROR: cannot verify raw.githubusercontent.com's certificate, issued by ‘CN=DigiCert SHA2 High Assurance Server CA,OU=www.digicert.com,O=DigiCert Inc,C=US’:
  Unable to locally verify the issuer's authority.
To connect to raw.githubusercontent.com insecurely, use `--no-check-certificate'.
$ wget https://raw.githubusercontent.com/arraytools/bdge/master/install_rnaseq.sh --no-check-certificate
--2017-02-26 08:41:26--  https://raw.githubusercontent.com/arraytools/bdge/master/install_rnaseq.sh
Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 151.101.192.133, 151.101.128.133, 151.101.0.133, ...
Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|151.101.192.133|:443... connected.
WARNING: cannot verify raw.githubusercontent.com's certificate, issued by ‘CN=DigiCert SHA2 High Assurance Server CA,OU=www.digicert.com,O=DigiCert Inc,C=US’:
  Unable to locally verify the issuer's authority.
HTTP request sent, awaiting response... 200 OK
Length: 8502 (8.3K) [text/plain]
Saving to: ‘install_rnaseq.sh’

install_rnaseq.sh                        100%[===============================================================================>]   8.30K  --.-KB/s    in 0.001s  

2017-02-26 08:41:26 (15.7 MB/s) - ‘install_rnaseq.sh’ saved [8502/8502]

Method 2: homebrew 

ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
brew install wget --with-libressl

Method 3: Build from source (require Xcode, works on my OS X 10.12 Sierra w/ Xcode 8.2.1) 

xcode-select --install
cd ~/Downloads

curl -O https://www.openssl.org/source/openssl-1.0.2h.tar.gz
tar xzvf openssl-1.0.2h.tar.gz
cd openssl-1.0.2h
./configure darwin64-x86_64-cc 
make
sudo make install

curl -O http://ftp.gnu.org/gnu/wget/wget-1.18.tar.gz # version 1.19 won't work at the 'make' step
tar -zxvf wget-1.18.tar.gz
cd wget-1.15/
./configure –with-ssl=openssl –with-libssl-prefix=/usr/local/ssl
make
sudo make install

For some reason, when I use wget to download files from https server, I will get a message: ERROR: cannot verify site certificate. Unable to locally verify the issuer’s authority. See

watch

http://stackoverflow.com/questions/9574089/osx-bash-watch-command 

while :; do clear; your_command; sleep 2; done

htop

http://unix.stackexchange.com/questions/98253/how-do-i-install-htop-inside-mac-os-x

md5sum

It is called md5 instead of md5sum in Linux.

For SHA-1 and SHA-256 use 

shasum filename
# OR
shasum -a 1 filename

shasum -a 256 filename

tar

If we run the following command 

tar xzvf filename.tar.gz -C directory 2> error.log

we will get a non-empty file in <error.log> even the extraction is successful.

Therefore it is better to use the following way 

tar xzvf filename.tar.gz -C directory
if [ $? -eq 0 ]; then
    echo OK
else
    echo FAIL
fi

Diff tools

  • Diff Tools on macOS
  • FileMerge - part of XCode from Apple. Too un-intuitive compared to WinMerge on Windows or Meld on Linux:(
  • DiffMerge. Still not intuitive.
  • Meld for OSX - BEST!
  • Beyond Compare (commercial)
  • Araxis Merge (commercial)
  • DeltaWalker (commercial)
  • Kaleidoscope (commercial)

R

failed to load cairo DLL

I got an error when I use svg() command. 

 svg("~/Downloads/3dPiePlot.svg")
Warning messages:
1: In svg("~/Downloads/3dPiePlot.svg") :
  unable to load shared object '/Library/Frameworks/R.framework/Resources/library/grDevices/libs//cairo.so':
  dlopen(/Library/Frameworks/R.framework/Resources/library/grDevices/libs//cairo.so, 6): Library not loaded: /opt/X11/lib/libXrender.1.dylib
  Referenced from: /Library/Frameworks/R.framework/Resources/library/grDevices/libs//cairo.so
  Reason: image not found
2: In svg("~/Downloads/3dPiePlot.svg") : failed to load cairo DLL

http://r.789695.n4.nabble.com/Cairo-package-error-quot-unable-to-load-quot-td4694453.html

you don't have X11 installed and it no longer ships with OS X 10.9 - you need to get it from

http://xquartz.macosforge.org

At the end of installation, it will ask you to log out and log in again to make xquartz a default X11 server.

Tex

Download failure

BasictexErr.png

The error seems to be related to a new release (6/7/2017). The download link for basicTex is http://tug.org/cgi-bin/mactex-download/BasicTeX.pkg. It downloaded the file mactex-basictex-20161009.pkg. But the new release is mactex-basictex-20170607.pkg. The download works fine on 6/8/2017.

http://ctan.org/pkg/mactex-basic website is working fine but the downloaded file name is <BasicTex.pkg> so it is not clear about the release date.

tlmgr error

$ tlmgr update --self
tlmgr: The Tex Live versions supported by the repository
http://ctan.sharelatex.com/tex-archive/systems/texlive/tlnet
  (2016-2016)
do not include the version of the local installation
  (2017).

Apple Server

OS Server

Hackintosh

How to Triple Boot Your Hackintosh with Windows and Linux

http://lifehacker.com/5698205/how-to-triple-boot-your-hackintosh-with-windows-and-linux

How To Install macOS Sierra Hackintosh On PC

http://www.redmondpie.com/how-to-install-macos-sierra-hackintosh-on-pc-guide/

Building a GTX 1080 Ti-powered Hackintosh: Installing macOS Sierra step-by-step

https://9to5mac.com/2017/04/28/building-a-gtx-1080-ti-powered-hackintosh-installing-macos-sierra-step-by-step-video/

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